1. Perl.
Preferably, ActivePerl from ActiveState. You should install it in
/usr/local/ActivePerl because thats where the programs assume it will be
found. If its installed, the following command
which perl
should give you /usr/local/ActivePerl/bin/perl
If you choose to install it in another place, you have to change the
path inside (the first line of the program)
2. Bioperl
Go to www.bioperl.org and download latest bioperl and install it. Without
bioperl-based most programs will not work.
3. Extra suggested perl modules can be installed. All these can be obtained
from http:/search.cpan.org
Error
Graphics::ColorUtils
Sort::Fields
Statistics::Descriptive
Text::ASCIITable
Graphics::ColorUtils
Regexp::Common
Sort::Versions
String::CRC
File::Tail
Bio::LITE::Taxonomy
if perl is installed properly, you can use ppm to install several of these modules
e.g.
apt-get install Sort::Fields
4. Some programs might use internally programs from the EMBOSS package. These programs
should be available in the path
for ubuntu users, install emboss like this..
apt-get install emboss
5. R package (get from CRAN http://www.r-project.org/ )
you should install the following R packages..
- Hmisc
- vegan
- FactoMineR
6. Other useful programs
- trimAL alignment trimming (http://trimal.cgenomics.org )
- trf tandem repeat finder (http://tandem.bu.edu/trf/trf.html)
- ssu-align 16s rRNA aligner (http://selab.janelia.org/software.html)
- hmmer3 http://selab.janelia.org/software.html
- mummer http://mummer.sourceforge.net/
7. You can copy the programs to a folder and make them executables, e.g.
chmod +x convertseq
make sure to add the location of these programs to your $PATH variable.